a2m2html output for file tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1999.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- T0098 Spo0A protein, B. stearothermophilus
- gi|1711477|sp|P52935|SP0A_BACTU_146:264 STAGE 0 SPORULATION PROTEIN A (Bacillus thuringiensis)
- gi|629165|pir||S47062 Spo0A protein - Bacillus thuringiensis (Bacillus thuringiensis)
- gi|580957|emb|CAA56683.1| (X80639) Spo0A [Bacillus thuringiensis] (Bacillus thuringiensis)
- gi|2654216|emb|CAA05307.1|_140:259 (AJ002297) Spo0A protein [Bacillus stearothermophilus] (Bacillus stearothermophilus)
- gi|134739|sp|P06534|SP0A_BACSU_148:267 STAGE 0 SPORULATION PROTEIN A (Bacillus subtilis)
- gi|72763|pir||SZBS0A stage 0 sporulation protein spo0A - Bacillus subtilis (Bacillus subtilis)
- gi|143585|gb|AAA22786.1| (M10082) spo0A sporulation protein (gtg start codon) [Bacillus subtilis] (Bacillus subtilis)
- gi|1303925|dbj|BAA12581.1| (D84432) Spo0A [Bacillus subtilis] (Bacillus subtilis)
- gi|2634856|emb|CAB14353.1| (Z99116) two-component response regulator [Bacillus subtilis] (Bacillus subtilis)
- gi|7576238|emb|CAB87985.1|_154:273 (AJ288947) Spo0A protein [Clostridium beijerinckii] (Clostridium beijerinckii)
- gi|1711479|sp|P52938|SP0A_CLODI_154:270 STAGE 0 SPORULATION PROTEIN A HOMOLOG (Clostridium difficile)
- gi|1174099|gb|AAB05561.1| (U43514) phosphorylation-activated transcription factor spo0a [Clostridium difficile] (Clostridium difficile)
- gi|7576241|emb|CAB87987.1|_173:292 (AJ288948) Spo0A protein [Clostridium cellulolyticum] (Clostridium cellulolyticum)
- gi|2119856|pir||S60880_151:269 phosphorylation-activated transcription factor Spo0A - Clostridium pasteurianum (Clostridium pasteurianum)
- gi|1711481|sp|P52940|SP0A_CLOPA_151:268 STAGE 0 SPORULATION PROTEIN A HOMOLOG (Clostridium pasteurianum)
- gi|497971|gb|AAA18883.1| (U09982) Spo0A [Clostridium pasteurianum] (Clostridium pasteurianum)
- gi|2119855|pir||S60874_145:263 phosphorylation-activated transcription factor Spo0A - Bacillus sphaericus (Bacillus sphaericus)
- gi|2144249|pir||S60879_149:267 phosphorylation-activated transcription factor Spo0A - Clostridium innocuum (Clostridium innocuum)
- gi|1711480|sp|P52939|SP0A_CLOIN_149:266 STAGE 0 SPORULATION PROTEIN A HOMOLOG (Clostridium innocuum)
- gi|497969|gb|AAA18882.1| (U09981) Spo0A [Clostridium innocuum] (Clostridium innocuum)
- gi|1174405|sp|P42012|SP0A_BACSH_145:262 STAGE 0 SPORULATION PROTEIN A (Bacillus sphaericus)
- gi|497959|gb|AAA18877.1| (U09976) Spo0A [Bacillus sphaericus] (Bacillus sphaericus)
- gi|2119850|pir||S60873_86:191 phosphorylation-activated transcription factor Spo0A - Bacillus pumilus (fragment) (Bacillus pumilus)
- gi|1711475|sp|P52933|SP0A_BACPU_85:190 STAGE 0 SPORULATION PROTEIN A (Bacillus pumilus)
- gi|497957|gb|AAA18876.1| (U09975) Spo0A [Bacillus pumilus] (Bacillus pumilus)
- gi|1130609|emb|CAA63989.1|_154:255 (X94328) spo0a [Clostridium difficile] (Clostridium difficile)
- gi|1711476|sp|P52934|SP0A_BACST_76:146 STAGE 0 SPORULATION PROTEIN A (Bacillus stearothermophilus)
- gi|497961|gb|AAA18878.1| (U09977) Spo0A [Bacillus stearothermophilus] (Bacillus stearothermophilus)
- gi|2119852|pir||S60875_77:147 phosphorylation-activated transcription factor Spo0A - Bacillus stearothermophilus (fragment) (Bacillus stearothermophilus)
- gi|2119851|pir||S60870_82:151 phosphorylation-activated transcription factor Spo0A - Bacillus cereus (fragment) (Bacillus cereus)
- gi|1711472|sp|P52930|SP0A_BACCE_81:150 STAGE 0 SPORULATION PROTEIN A (Bacillus cereus)
- gi|497951|gb|AAA18873.1| (U09972) Spo0A [Bacillus cereus] (Bacillus cereus)
- gi|2119857|pir||S60868_146:215 phosphorylation-activated transcription factor Spo0A - Bacillus anthracis (fragment) (Bacillus anthracis)
- gi|1711470|sp|P52928|SP0A_BACAN_145:214 STAGE 0 SPORULATION PROTEIN A (Bacillus anthracis)
- gi|497947|gb|AAA18871.1| (U09970) Spo0A [Bacillus anthracis] (Bacillus anthracis)
- gi|2119858|pir||S60871_142:211 phosphorylation-activated transcription factor Spo0A - Bacillus circulans (fragment) (Bacillus circulans)
- gi|1711474|sp|P52932|SP0A_BACME_143:212 STAGE 0 SPORULATION PROTEIN A (Bacillus megaterium)
- gi|497955|gb|AAA18875.1| (U09974) Spo0A [Bacillus megaterium] (Bacillus megaterium)
- gi|2119859|pir||S60872_144:213 phosphorylation-activated transcription factor Spo0A - Bacillus megaterium (fragment) (Bacillus megaterium)
- gi|1711473|sp|P52931|SP0A_BACCI_141:210 STAGE 0 SPORULATION PROTEIN A (Bacillus circulans)
- gi|497953|gb|AAA18874.1| (U09973) Spo0A [Bacillus circulans subsp. circulans] (Bacillus circulans subsp. circulans)
- gi|1711478|sp|P52937|SP0A_CLOBU_92:161 STAGE 0 SPORULATION PROTEIN A HOMOLOG (Clostridium butyricum)
- gi|497967|gb|AAA18881.1| (U09980) Spo0A [Clostridium butyricum] (Clostridium butyricum)
- gi|2119853|pir||S60878_93:162 phosphorylation-activated transcription factor Spo0A - Clostridium butyricum (fragment) (Clostridium butyricum)
- gi|1711498|sp|P52936|SP0A_CLOAB_154:223 STAGE 0 SPORULATION PROTEIN A HOMOLOG (Clostridium acetobutylicum)
- gi|497965|gb|AAA18880.1| (U09979) Spo0A [Clostridium acetobutylicum] (Clostridium acetobutylicum)
- gi|2119861|pir||S60877_155:224 phosphorylation-activated transcription factor Spo0A - Clostridium acetobutylicum (strain NCIMB 8052) (fragment) (Clostridium acetobutylicum)
- gi|1711471|sp|P52929|SP0A_BACBR_144:212 STAGE 0 SPORULATION PROTEIN A (Brevibacillus brevis)
- gi|2119860|pir||S60869 phosphorylation-activated transcription factor Spo0A - Bacillus brevis (fragment) (Brevibacillus brevis)
- gi|497949|gb|AAA18872.1| (U09971) Spo0A [Brevibacillus brevis] (Brevibacillus brevis)
- gi|497963|gb|AAA18879.1|_97:166 (U09978) Spo0A [Clostridium acetobutylicum] (Clostridium acetobutylicum)
- gi|2119854|pir||S60876_98:167 phosphorylation-activated transcription factor Spo0A - Clostridium acetobutylicum (ATCC 4259) (fragment) (Clostridium acetobutylicum)
- gi|1020324|gb|AAA79509.1|_85:154 (U36481) sporulation protein homolog [Clostridium difficile] (Clostridium difficile)
- gi|1711482|sp|P52941|SP0A_MOOTH_137:206 STAGE 0 SPORULATION PROTEIN A HOMOLOG (Moorella thermoacetica)
- gi|497973|gb|AAA18884.1| (U09983) Spo0A [Moorella thermoacetica] (Moorella thermoacetica)
- gi|2119862|pir||S60881_138:207 phosphorylation-activated transcription factor Spo0A - Clostridium thermoaceticum (fragment) (Moorella thermoacetica)

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 DNKPKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR
   2 --KPKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR
   3 -NKPKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR
   4 -PKKKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASR
   5 -KAPIDLETEITNIIHEVGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR
   6 -KNVGNIETEITNIIHEIGVPAHIKGYLYLREAMKMVIDNVELLGAVTKELYPSIAKKFNTTPSR
   7 -NTSRSLEVEVTNVMHEIGVPAHIKGYQYLRDAIMMVVKDLDVINSITKLLYPSIAKEYNTTPSR
   8 -QSNVPLDLEDESIIHEIGVPAHIKGYMYLREAINMVVDNIELLSAVTKELYPSIAKKYNTTASR
   9 --QSVPLDLEDESIIHEIGVPAHIKGYMYLREAINMVVDNIELLSAVTKELYPSIAKKYNTTASR
  10 -NQQHQLDSTITAIIKEIGVPAHIKGYSYLREAIQMVFEDIELLGSVTKILYPEIAKKFNTTPSR
  11 -QKYLELESEITELLHEIGIPAHIKGYMYLRTAILETYLNVDFLGQITKVLYPEIAKKYATTASR
  12 --QKLELESEITELLHEIGIPAHIKGYMYLRTAILETYLNVDFLGQITKVLYPEIAKKYATTASR
  13 --NQHQLDSTITAIIKEIGVPAHIKGYSYLREAIQMVFEDIELLGSVTKILYPEIAKKFNTTPSR
  14 -KRNKNLDASITTIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASR
  15 -PKRKNLDASITTIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASR
  16 -KNVGNIETEITNIIHEIGVPAHIKGYLYLREAMKMVIDNVELLGAVTKELYPSIAKKFNTTPSR
  17 DNKPKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR
  18 NKPKKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR
  19 -KPKKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR
  20 -GKPKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR
  21 -KPKKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR
  22 -GKPKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR
  23 -KTKKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR
  24 -SKPANLDASITSIIHEIGVPAHIKGYLYLREAISMVYKDIELLGSITKVLYPDIAKKYNTTASR
  25 -KPQANLDASITSIIHEIGVPAHIKGYLYLREAISMVYKDIELLGSITKVLYPDIAKKYNTTASR
  26 -PKTKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR
  27 -KTPVDLETEITNIIHEIGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR
  28 -TPSVDLETEITNIIHEIGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR
  29 -KAPIDLETEITNIIHEVGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR
  30 -APSIDLETEITNIIHEVGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR
  31 --RGRNLDASITSIIHEIGVPAHIKGYLYLREAITMVYNDVELLGSITKVLYPDIAKKFNTTASH
  32 -NKAVDLESEITSIIHQIGVPAHIKGYMYLREAITMVVNNMELLSAVTKELYPSIAKKYNTTASR
  33 -KANVDLESEITSIIHQIGVPAHIKGYMYLREAITMVVNNMELLSAVTKELYPSIAKKYNTTASR
  34 -KNVGNIETEITNIIHEIGVPAHIKGYLYLREAMKMVIDNVELLGAVTKELYPSIAKKFNTTPSR
  35 -RAGRNMDVEVTKIIHQMGVPAHIKGYQYLREAILMVIDDVSLLGAVTKELYPLIARKYMTTPSR
  36 -AGGRNMDVEVTKIIHQMGVPAHIKGYQYLREAILMVIDDVSLLGAVTKELYPLIARKYMTTPSR


         70        80        90       100       110       120 
         |         |         |         |         |         | 
   1 VERAIRHAIEVAWSRGNLESISSLFGYTVSVSKAKPTNSEFIAMVADKLRLEHKAS
   2 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMSKAKPTNSEFIAMVADKLRLEHKAS
   3 VERAIRHAIEVAWSRGNLESISSLFGYTVSVSKAKPTNSEFIAMVADKLRLEHKAS
   4 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMTKAKPTNSEFIAMVADKLRLEHKAS
   5 VERAIRHAIEVAWGRGQIEAINRLFGYTVHNDKGKPTNSEFIAIIADKLRLKNKVS
   6 VERAIRHAIEVAWSRGKVDTINQLFGYTVHNTKGKPTNSEFIAMIADKLRLEH---
   7 VERAIRHAIEVAWSRGQVEAIDALFGYTVNIGKGKPTNSEFIAMIADKLRLELKVS
   8 VERAIRHAIEVAWSRGQVDTINKLFGYTIHNGKGKPTNSEFIAMIADKLRLKNKV-
   9 VERAIRHAIEVAWSRGQVDTINKLFGYTIHNGKGKPTNSEFIAMIADKLRLKNKV-
  10 VERAIRHAIEVAWNRGNYEYISSMFGYTEHHLKSKPTNSEFIAMIADKIRIDMMA-
  11 VERAIRHAIEVAWNRGNIDAIDDIFGYTISASKAKPTNSEFIAMISDKLRLEHRL-
  12 VERAIRHAIEVAWNRGNIDAIDDIFGYTISASKAKPTNSEFIAMISDKLRLEHRL-
  13 VERAIRHAIEVAWNRGNYEYISSMFGYTEHHLKSKPTNSEFIAMIADKIRIDMMA-
  14 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMSKAKPTNSEFI--------------
  15 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMSKAKPTNSEFI--------------
  16 VERAIRHAIEVAWSRGKVDTINQLFGYTVHNTKGKPTN------------------
  17 VERAIR--------------------------------------------------
  18 VERAIR--------------------------------------------------
  19 VERAIR--------------------------------------------------
  20 VERAIR--------------------------------------------------
  21 VERAIR--------------------------------------------------
  22 VERAIR--------------------------------------------------
  23 VERAIR--------------------------------------------------
  24 VERAIR--------------------------------------------------
  25 VERAIR--------------------------------------------------
  26 VERAIR--------------------------------------------------
  27 VERAIR--------------------------------------------------
  28 VERAIR--------------------------------------------------
  29 VERAIR--------------------------------------------------
  30 VERAIR--------------------------------------------------
  31 VERAIR--------------------------------------------------
  32 VERAIR--------------------------------------------------
  33 VERAIR--------------------------------------------------
  34 VERAIR--------------------------------------------------
  35 VERAIR--------------------------------------------------
  36 VERAIR--------------------------------------------------